06/06, 2022
Introduction
What is reproducible research?
- Interlaced code, data (Raw) and text
- Repos on github
- in R: Rmarkdown (Rmd)
Reproducibility en R
- A folder
- Raw data (csv, xls, html, json)
- Code and text (Rmd, shiny)
- Results (Manuscript, Web Page, App)
Some motivation
- The webpage of a project
- interactive plots and documents.
- Presentations with interactive elements
- Full manuscripts
External Resources
- Rmarkdown the ultimate guide
- Cheat sheet
Objectives
Objectives
- Part 1: Set up the project and rmarkdown basics
- Part 2: getting the most of your rmd by using interactive HTML
- Part 3: Reusing code for presentations and PDfs
Part 1 Set up the project and rmarkdown basics
In this part
- Start a new project
- Generate your github repo
- Generate your readme file
- Simple html report
Start a new project and generate your github repo
usethis::use_git() # set your credentials if you must gitcreds::gitcreds_set() # if you dont have a pat you can use usethis::create_github_token() # if you need add your PAT usethis::edit_r_environ() # generate your readme usethis::use_readme_rmd() # Edit and upload to git usethis::use_github()
lets get the dataset
Variables:
- lon: Longitude in decimal degrees
- Lat: Latitude in decimal degrees
- bio_1 to bio_19 bioclimatic variables as defined in worldclim
- abund_sp1 to abund_sp4: abundance of species 1, 2 and 4
Basic rmarkdown
- Text
- Chunks
- Inline code
- Cheat sheet Rmd
- The magic button Knit
Text
# Title ## subtitle *cursive* **bold** [link](https://stackoverflow.com/users/3808018/derek-corcoran)
Chunks
knitr::include_graphics("Chunk.png")
- echo = T o F show code
- message = T o F shows message of packages
- warning = T o F shows or does not show warning
- eval = T o F runs or does not run the code
- cache = T o F saves the result or not
- For more options check this link
Inline code
Inline
- Code interlinked with text
- To update means, maximum, minimum
- p-values, statistical differences
- They can be vectors, and not tables.
State the objective of the project in your readme
- include a chunk
- include an inline code
- include a graph
- try to include a table
05:00
First look at the dataset
First look at the dataset (cont.)
First html report
More advanced rmarkdown
Get the template in this link
- Includes the use of references
- Crossrefences of tables, figures, equations, etc
- More in the bookdown package gitbook
- Includes example of the kableExtra package
Second activity
- Document in your readme the creation of this document and it’s objective
- Generate graphs and tables for your project and make crossreferences
- Change the style of your bibliography using csl
- Until 10 am